title: Sm_NecHi_Log_Rep3

description:
Sm_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Human FL Tfh gene-level [PGD_913_HTA]

status: Public on May 29 2024

type: RNA

city: Rennes

first: Stephane

last: Rodriguez

state: France

address: 2, Av Pr. Leon Bernard

country: France

institute: INSERM

description:
PGD_913_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis

hyb_protocol: 4.7 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Human Transcriptome Array 2.0 (Affymetrix). The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: Chip were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.3.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Follicular Lymphoma donor

label_protocol: Biotinylated double strand cDNA targets were prepared, starting from 25 ng of total RNA for all samples except PGD-926 for which we used 15 ng, with the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol:
Lymphoid cells were recovered by perfusion of FL lymph node (LN) biopsies or non-malignant tonsils, enriched using Ficoll gradient
First, CD19+/CD14+/CD8+/CD16+ cell populations were targeted by their dedicated mouse anti-human monoclonal antibody, Second : an incubation with goat anti-mouse magnetic beads allowed CD4+ T enrichement. Third, subsets of interest were sorted according to their known phenotype using a FACSAria flow cytometer
RNA was isolated from 0,5 to 10M sorted cells with the RNeasy AllPrep Micro Kit (Qiagen), according to the manufacturer’s instructions.

tag: tissue

value: Lymph node


title: Human FL Tfh gene-level [PGD_925_HTA]

description:
PGD_925_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Sm_NecHi_Log_Rep2

type: SRA

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

country: USA

institute: University of Maryland - Baltimore County

description:
Sm_NecHi_TPM.csv
Necromass_DEG.xlsx

library_source: transcriptomic

data_processing:
The raw FASTQ files were quality checked, aligned to existing genomes, and analyzed for differential expression using the Galaxy platform. Unless otherwise noted below, default parameters were in all analysis tools used except in cases where strandedness was specified (all RNAseq data were unstranded). Briefly, RNAseq data were concatenated using the concatenate data sets: tail-to-head (cat) tool. Transcript quality was tested using FastQC, which indicated read trimming was unnecessary for any of the files. Transcripts were next aligned to their respective reference genomes using the HISAT2 tool and quantified using the htseq-count tool. Reference genome files for C. japonicus Ueda107 (ASM1922v1) and C. pinensis DSM2588 (ASM2400v1) were obtained from ENSEMBLE, while that for S. marcescens PIC3611 was retrieved from NCBI Refseq (ASM2260299v1). Due to the differences in reference genome sources, the S. marcescens files required a parameter change in the htseq-count ‘feature type’ from ‘gene’ to ‘exon’. Differential gene expression using DESeq2 compared necromass exponential growth to necromass stationary phase for all three species and glucose for Cp and Sm.
Assembly: C. japonicus Ueda107 (ASM1922v1); C. pinensis DSM2588 (ASM2400v1); S. marcescens PIC3611 (ASM2260299v1)
Supplementary files format and content: TPM for biolgical repliates for a given substrate and bacterial species; DEG with p-values for pair-wise comparisons

organism: Serratia marcescens

source_name: Bacterial cell

extract_protocol:
As per the protocol described in PMID: 22949721
Ribosomal RNA Depletion; RNA Fragmentation and Random Priming; Fist and Second Strand cDNA synthesis; End Repair with 5' phosphorylation and dA-Tailing; Adapter ligation with PCR enrichment; Sequencing

tag: strain

tag: cell type

value: Bacterial cell

tag: genotype

value: WT

tag: group

value: NecHi

tag: growth phase

value: Log


title: Human tonsil Naive CD4 gene-level [PGD_910_HTA]

description:
PGD_910_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis

source_name: Healthy donor

value: tonsil


title: Human tonsil Tfh gene-level [PGD_909_HTA]

description:
PGD_909_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: RNA Mir-146 KO/Empty 3

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: Mir-146 KO/Empty 3

data_processing:
FastQC (v0.11.2) was used to test reads quality.
Paired-end reads were aligned against mm10 genome using HISAT (v2.0.4).
Gene counts were summarized using featureCounts (v1.5.2)
Assembly: mm10
Supplementary files format and content: IGEAK_rawCounts.csv, iGEAK_annotation.csv, iGEAK_metadata.csv
Supplementary files format and content: Tab-delimted raw gene counts, sample info, and gene annotation matrices

organism: Mus musculus

source_name: Bone Marrow

growth_protocol: GFP+ LSK cells were FACS sorted directly in RLT buffer

extract_protocol:
Total RNA was extracted from the sorted GFP+/lin-/ckit+/Sca+ cells cells using RNeasy Plus Micro Kit (Qiagen).
The initial amplification step for all samples was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. The concentrations were measured using the Qubit dsDNA BR assay. Libraries were then created for all samples using the Illumina protocol (Nextera XT DNA Sample Preparation Kit). The concentrations were measured using the Qubit dsDNA HS assay. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The concentration of the pool was optimized to acquire at least 15-20 million reads per sample.

value: Bone Marrow

tag: cell line

value: primary cell

value: Hematopoietic stem and progenitor cell


title: Sm_NecHi_Log_Rep1

description:
Sm_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Sm_Glc_Sta_Rep3

description:
Sm_Glc_TPM.csv
Necromass_DEG.xlsx

value: Glc

value: Sta


title: Human tonsil Memory CD4 gene-level [PGD_908_HTA]

description:
PGD_908_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human tonsil Treg gene-level [PGD_911_HTA]

description:
PGD_911_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human tonsil Treg gene-level [PGD_907_HTA]

description:
PGD_907_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: RNA Mir-146 KO/Empty 1

description: Mir-146 KO/Empty 1


title: Human tonsil Memory CD4 gene-level [PGD_912_HTA]

description:
PGD_912_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: RNA Empty 3

description: Empty 3

value: miR-146a wildtype/Runx1 wildtype


title: Sm_Glc_Sta_Rep2

description:
Sm_Glc_TPM.csv
Necromass_DEG.xlsx


title: RNA Empty 2

description: Empty 2


title: RNA Empty 1

description: Empty 1


title: Sm_Glc_Sta_Rep1

description:
Sm_Glc_TPM.csv
Necromass_DEG.xlsx


title: Human tonsil Tfh gene-level [PGD_905_HTA]

description:
PGD_905_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: RNA Runx1 3

description: Runx1 3


title: RNA Runx1 1

description: Runx1 1


title: RNA Runx1 2

description: Runx1 2


title: Sm_Glc_Log_Rep2

description:
Sm_Glc_TPM.csv
Necromass_DEG.xlsx


title: Sm_Glc_Log_Rep3

description:
Sm_Glc_TPM.csv
Necromass_DEG.xlsx


title: RNA Runx1 Mir-146 KO 3

description: Runx1 Mir-146 KO 3


title: RNA Runx1 Mir-146 KO 1

description: Runx1 Mir-146 KO 1


title: RNA Runx1 Mir-146 KO 2

description: Runx1 Mir-146 KO 2


title: RNA Mir-146 KO/Empty 2

description: Mir-146 KO/Empty 2


title: Human tonsil Naive CD4 gene-level [PGD_906_HTA]

description:
PGD_906_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: spleen, challenged, predicted to die, ms35

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Sequence quality was assessed using FastQC v0.11.5 and MultiQC v0.8.
The FASTQ sequence reads were aligned to the mouse genome (Ensembl GRCm38.94) using STAR v2.5 and mapped to Ensembl transcripts.
Read-counts were generated using htseq-count (HTSeq 0.6.1p1).
Assembly: Ensembl GRCm38.94

molecule: polyA RNA

source_name: spleen

extract_protocol:
Total RNA was extracted from each sample using the RiboPure RNA purification kit
Poly-adenylated RNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog no.: E7409L, NEB). Strand-specific cDNA libraries were generated from poly-adenylated RNA using the KAPA Stranded RNA-Seq Library Preparation Kit (cat. no.: 07277253001, Roche).

value: spleen

tag: condition

value: challenged, predicted to die


title: spleen, challenged, predicted to die, ms33


title: spleen, challenged, predicted to die, ms31


title: spleen, challenged, predicted to die, ms32


title: spleen, challenged, predicted to die, ms30


title: spleen, challenged, predicted to survive, ms29

value: challenged, predicted to survive


title: Resting AECs, Subject 4

city: Boston

first: Nora

last: Barrett

state: Massachussetts

address: 60 Fenwood Rd

department: Allergy and Clinical Immunology

institute: Brigham and Women’s Hospital

data_processing:
FASTQ files were aligned to the  human genome using STAR (v2.7.9a) with standard parameters and two-pass mode.
BAM files generated with STAR and counts were calculated using RSEM (v1.3.3).
We normalized the counts by transforming them to their log2(TPM+1) value, where TPM stands for transcripts per million.
Assembly: GRCh38
Supplementary files format and content: Counts.txt contains expected gene counts as calculated by RSEM.
Supplementary files format and content: Log2TPM.txt contains TPM values as calculated by RSEM that were then scaled to log2(tpm+1).

source_name: Airway epithelial cells

growth_protocol: Air-liquid interface (ALI) cultures were grown from nasal basal epithelial cells from healthy adult donors. ALIs were allowed to mature for 14 days, then stimulated with 10 ng/mL of IL-4 and 10 ng/mL of IL-13 for an additional 7 days.

extract_protocol:
Cells were lysed with TCL buffer (Qiagen 1031576) and lysates were stored at -80C
SmartSeq2 protocol was used to extract low-input bulk RNA-seq and libraries were later submitted to the Broad Insitute for 38bp paired-end sequencing.

value: Airway epithelial cells

tag: subject

value: E

tag: age

tag: Sex

value: Female

tag: treatment

value: Control


title: spleen, challenged, predicted to survive, ms27


title: Resting AECs, Subject 3

value: B

value: Male


title: spleen, challenged, predicted to die, ms28


title: Sm_Glc_Log_Rep1

description:
Sm_Glc_TPM.csv
Necromass_DEG.xlsx

value: Bacterial cell

value: WT

value: Log


title: spleen, challenged, predicted to survive, ms26


title: Resting AECs, Subject 2

value: D


title: spleen, challenged, predicted to survive, ms25


title: spleen, challenged, predicted to die, ms20


title: spleen, challenged, predicted to survive, ms23


title: spleen, challenged, predicted to die, ms19


title: Resting AECs, Subject 1

value: A


title: AECs co-stimulated in vitro with IL-4 and  IL-13, Subject 4


title: spleen, challenged, predicted to survive, ms17


title: Resting AECs, Subject 5

value: F


title: AECs co-stimulated in vitro with IL-4 and  IL-13, Subject 5


title: spleen, challenged, predicted to die, ms16


title: spleen, non-challenged, control, ms24

value: non-challenged, control


title: AECs co-stimulated in vitro with IL-4 and  IL-13, Subject 3


title: spleen, challenged, predicted to survive, ms18


title: spleen, non-challenged, control, ms15


title: spleen, challenged, predicted to survive, ms13


title: AECs co-stimulated in vitro with IL-4 and  IL-13, Subject 2


title: spleen, challenged, predicted to die, ms12


title: AECs co-stimulated in vitro with IL-4 and  IL-13, Subject 1


title: NOK-2

city: Chengdu

first: Yangfan

last: Liu

state: Sichuan

address: People South Street

country: China

institute: Sichuan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: NOK

growth_protocol: Cal27 cells were cultured in DMEM (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum, while NOK cells were cultured in Defined Keratinocyte SFM (Gibco, Grand Island, NY, USA) supplemented with a concentration of 0.4% EGF. All cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: All cells were not treated

value: NOK

value: normal


title: NOK-3


title: spleen, challenged, predicted to survive, ms10

value: spleen


title: spleen, challenged, predicted to die, ms08

value: challenged, predicted to die


title: spleen, non-challenged, control, ms04


title: Cal27-3

value: OSCC


title: NOK-1


title: Cal27-2


title: liver, challenged, predicted to die, ms33

source_name: liver

value: liver


title: spleen, non-challenged, control, ms02


title: Cal27-1


title: liver, challenged, predicted to survive, ms29

value: challenged, predicted to survive


title: liver, challenged, predicted to die, ms30


title: liver, challenged, predicted to die, ms32


title: GWP_Donor_C

city: Singapore

first: Wei-Xiang

last: Sin

address: 1 CREATE Way, #04-13/14, Enterprise Wing

country: Singapore

institute: SMART

data_processing:
Paired-end clean reads, which were > 97% of raw reads, were aligned to the hg38 reference genome using Hisat2 (v2.0.5). Uniquely mapped reads, which were > 93% of total reads, were used for subsequent quantitative data analysis. featureCounts (v1.5.0-p3) was used to count the read numbers mapped to each gene, and then gene expression levels (FPKM) of each gene were calculated.
Assembly: hg38
Supplementary files format and content: .xls file of read counts
Supplementary files format and content: .xls file of FPKM values

source_name: T cell

growth_protocol: T cells were produced in microbioreactor (MBR) versus gas-permeable well plate (GWP)

extract_protocol:
Total RNA were extracted using PureLink RNA Mini Kit (Thermo Fisher Scientific)
NEBNext Ultra Directional RNA Library Prep Kit for Illumina. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, followed by fragmentation, first strand cDNA synthesis using random hexamer primers, second strand cDNA synthesis using dUTP, end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, cDNA amplification, and purification.

value: T cell


title: liver, challenged, predicted to die, ms31


title: liver, challenged, predicted to survive, ms27


title: liver, challenged, predicted to die, ms28


title: spleen, non-challenged, control, ms03


title: GWP_Donor_B


title: liver, challenged, predicted to survive, ms25


title: liver, challenged, predicted to survive, ms26


title: GWP_Donor_A


title: spleen, non-challenged, control, ms06


title: spleen, challenged, predicted to die, ms07


title: spleen, non-challenged, control, ms01


title: MBR_Donor_C


title: liver, challenged, predicted to die, ms20


title: liver, challenged, predicted to die, ms19


title: liver, challenged, predicted to die, ms35


title: liver, non-challenged, control, ms24


title: liver, challenged, predicted to survive, ms18


title: ES2-EC359- 2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: ES2 cells treated with LIFR inhibitor EC359

growth_protocol: ES2 cells were cultured in RPMI media supplemented with 10% FBS

extract_protocol:
ES2 cells are treated with vehicle (0.1% DMSO) or EC359 (10 nM) for 12 hours and total RNA was isolated using RNeasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 500ng were used for sequencing library preparation according to Illumina TruSeq Stradned mRNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from ES2 cells that are treated with vehicle or EC359 and subjected to RNAseq analysis

value: Ovarian cancer cell line


title: MBR_Donor_A


title: liver, challenged, predicted to die, ms16


title: liver, non-challenged, control, ms15


title: liver, challenged, predicted to survive, ms13


title: liver, challenged, predicted to die, ms12


title: liver, challenged, predicted to survive, ms10


title: liver, challenged, predicted to die, ms08


title: R1000

city: Suzhou

first: Yidi

last: Wang

address: Ren'ai Road

department: School of Radiation Medicine and Protection

institute: Soochow University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh37
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: BEAS-2B cell line

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: BEAS-2B cell line

value: Irradiated by 1 Gy


title: R10

value: Irradiated by 10 mGy


title: R100

value: Irradiated by 100 mGy


title: liver, challenged, predicted to die, ms07


title: liver, non-challenged, control, ms04


title: R0

value: Without radiation


title: liver, non-challenged, control, ms06


title: liver, non-challenged, control, ms03


title: HEK293T_CUT&Tag_hg19_input

city: Shanghai

first: Xinyu

last: Cui

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
Quality checks with FastQC, the reads were aligned to human hg19 reference genome using Bowtie2 (v.2.5.0) tool with the configuration of bowtie2 -q -N 0 -L 22.
Peak calling was performed using the model-based analysis of ChIP–seq (MACS2 v.2.2.9.1) with the following configuration: MACS2 callpeak -f BAM -g 2.7e+9 –n BG4 CUT&Tag.
Integrative Genomics Viewer (IGV) was used to visualize the CUT&Tag signal.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
2 × 105 cells were treated with NE1 buffer (20 mM HEPES-KOH pH7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% (v/v) Triton X-100, 20% (v/v) Glycerol ) on ice for 10 minutes, then fixed with 0.1% formaldehyde in PBS for 2 min and harvested. The cells were washed with PBS, and immobilized to Concanavalin A Magnetic Beads (Beyotime, P2156) with incubation at room temperature for 10 min. The bead-bound cells were incubated in 200 μL of primary antibody buffer (20 mM HEPES-KOH pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1% (v/v) BSA, 2 mM EDTA) with 40 μl 0.05 mg/mL FLAG-tagged BG4 antibody or 2 μL 1 mg/mL Mouse IgG Isotype Control (Share-bio, SB-A00001) antibody at 4 ℃ by rotating overnight. The next day, Flag-Tag Mouse Monoclonal Antibody (Share-bio, SB-AB0008), Rabbit Anti-Mouse IgG H&L antibody (Bioss, bs-0296R), pA-Tn5 adapter complex were incubated at 37 ℃ for 1 hr. All three antibodies are diluted 1:200. Flag-Tag Mouse Monoclonal Antibody and Rabbit Anti-Mouse IgG H&L antibody were diluted with BSA-wash buffer (20 mM HEPES-KOH pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1% (v/v) BSA), and pA-Tn5 adapter complex was diluted with BSA-300 buffer (20 mM HEPES-KOH pH7.5, 300 mM NaCl, 0.5 mM Spermidine, 1% (v/v) BSA). After each incubation of antibodies, wash 3 times with the corresponding antibody incubation solution for 5 min. Tagmentation was performed with 50 μL Tagmentation buffer in 37℃ for 1 hr (20 mM HEPES-KOH pH7.5, 300 mM NaCl, 0.5 mM Spermidine, 1% (v/v) BSA, 10 mM MgCl2). After tagmentation, 1 μL 500 mM EDTA, 1 μL 20 mg/mL proteinase K and 1 μL 10% (w/v) SDS were added and further incubated in 55 ℃ for 1 hr and 70℃ for 20 minutes to stop tagmentation and digest protein. 122 μL DNA Selection Beads (Yeason, 12601ES) were added to the supernatant of the aforementioned process. Wash twice in 80% ethanol and elute the DNA using 35 μL TE buffer.
To generate G4 libraries, purified genomic DNA was amplified with the universal i5 primer and barcoded i7 primer using NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were electrophoresed using 2% (w/v) agarose gel and 200-500 bp size fragments were recovered with Gel Extraction Kit (Sangon Biotech, B511139). Sequencing were conducted on an Illumina Novaseq-PE150 instrument.
Cleavage under targets and tagmentation (CUT&Tag)

value: Human embryonic kidney

tag: chip antibody


title: liver, non-challenged, control, ms02


title: HEK293T_BG4_CUT&Tag_hg19_rep2

value: BG4(in-house preparation); Flag-Tag Mouse Monoclonal Antibody (Share-bio, SB-AB0008)


title: liver, non-challenged, control, ms01

value: non-challenged, control


title: MBR_Donor_B


title: blood, challenged, predicted to die, ms33

source_name: whole blood

value: whole blood


title: blood, challenged, predicted to die, ms35


title: HEK293T_BG4_CUT&Tag_hg19_rep1


title: blood, challenged, predicted to die, ms32


title: liver, challenged, predicted to survive, ms17


title: blood, challenged, predicted to die, ms30


title: blood, challenged, predicted to die, ms31


title: blood, challenged, predicted to die, ms28


title: HUVEC- Ta3-2

city: Beijing

first: Yunshu

last: Wu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/ hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: xenograft

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: xenograft

value: HUVEC

value: WT

value: cultured with Zr58Cu25Al14Ta3


title: blood, challenged, predicted to survive, ms29


title: blood, challenged, predicted to survive, ms25


title: blood, challenged, predicted to survive, ms27


title: blood, challenged, predicted to survive, ms26


title: HUVEC- Ta3-1


title: HUVEC- Ta0-3

value: cultured with Zr61Cu25Al14


title: HUVEC- Ta3-3


title: blood, challenged, predicted to survive, ms23

value: challenged, predicted to survive


title: blood, challenged, predicted to die, ms20

value: challenged, predicted to die


title: blood, non-challenged, control, ms24


title: HUVEC- Ta0-2


title: HUVEC- Ta0-1


title: blood, challenged, predicted to die, ms19


title: blood, challenged, predicted to survive, ms18


title: blood, challenged, predicted to survive, ms17


title: HUVEC- cpTi3

value: cultured with cpTi


title: blood, non-challenged, control, ms15


title: blood, challenged, predicted to die, ms16


title: blood, challenged, predicted to die, ms12


title: HUVEC- cpTi2


title: HUVEC- cpTi1


title: blood, challenged, predicted to survive, ms13


title: blood, challenged, predicted to die, ms08


title: blood, challenged, predicted to die, ms07


title: blood, challenged, predicted to survive, ms10


title: blood, non-challenged, control, ms04


title: blood, non-challenged, control, ms03


title: BMSC- Ta3-3

source_name: jaw bone

value: jaw bone

value: primary cells

value: bone marrow mesenchymal stem cells


title: blood, non-challenged, control, ms02


title: blood, non-challenged, control, ms01


title: BMSC- Ta3-1


title: RBG26490_Plate_4_WT

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

library_source: transcriptomic single cell

data_processing:
RNA-seq reads were aligned to mm10 + ERCC92 using GSNAP (version 2018-03-25) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.9.1) with the parameter (-s no).
Assembly: GRCm38.81
Supplementary files format and content: HTSeq counts text file with raw counts and htseq metrics
Supplementary files format and content: Anndata h5 file with filtered cells and genes and data transformations (in layers)

source_name: bone marrow

extract_protocol:
Bone marrow cells were harvested from STAT5KO and WT control mice, single ESLAM HSCs was FACS sorted into 2.3ul 0.2% Triton-100 containg RNAse inhibitor
Tagmentation is carried out using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm.

value: bone marrow

value: ESLAM


title: RBG26489_Plate_4_KO

value: KO


title: BMSC- Ta0-2


title: BMSC- Ta0-1


title: RBG26491_Plate_4_WT


title: RBG26492_Plate_4_WT


title: BMSC- cpTi3


title: RBG26493_Plate_4_WT


title: RBG26494_Plate_4_WT


title: BMSC- cpTi2


title: RBG26495_Plate_4_WT


title: RBG26480_Plate_4_WT


title: RBG26481_Plate_4_WT


title: BMSC- cpTi1


title: blood, non-challenged, control, ms06


title: BMSC- Ta3-2


title: RBG26488_Plate_4_KO


title: RBG26485_Plate_4_KO


title: RBG26482_Plate_4_WT


title: 100 nM OA_rep3

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
Demultiplexing of sequencing reads was accomplished using Illumina bcl2fastq (version 2.20).
Reads were classified as ribosomal RNA (rRNA) and removed by RiboDetector (version 0.2.7).
Quality and adapter trimming was done by fastp (version 0.20.0).
Reads were aligned to the human genome (hg38, UCSC) using STAR (version 2.7.8a) and quantified per gene ID by RSEM (version 1.3.3). In case of a few samples (LMK_1, LMK_3, OA33_3 and OA100_3) multiple fastq files were merged before mapping.
After removing genes with low expression (sum of reads across all samples below ten), 22122 genes were retained and analyzed by the R-package DESeq2 version 1.42.0 using default settings estimation of size factors and dispersion.
Negative Binomial GLM fitting and Wald statistics were applied to test for differential gene expression between each treatment and control conditions, respectively.
False discovery rate (FDR) was used to control for multiple testing. Only genes with a q-value ≤ 0.1 and absolute log2 fold change > 1 were included in the further analyses.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for all genes and samples (raw_read_counts.tsv)
Supplementary files format and content: tab-delimited text file contains normalized counts for filtered genes and all samples (normalized_counts.tsv)

source_name: HepaRG

growth_protocol: HepaRG cells were seeded in 6-well-plates (200 00 cells per well) and cultivated and proliferated in Williams E medium with 2 mM glutamine supplemented with 10 % fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, 0.05 % human insulin and 50 µM hydrocortison. After a 2-week proliferation phase, cells were differentiated in the mentioned culture medium additionally containing 1.7 % DMSO, for another 2 weeks.

extract_protocol:
RNA isolation was performed with the RNeasy Mini Kit (Qiagen) according to the manufactures' protocol.
Libraries were prepared from 100 ng of RNA using the TruSeq Stranded Total RNA kit (Illumina)

treatment_protocol: Differentiated cells were treated with the marine biotoxin okadaic acid (OA) at the non-cytotoxic concentrations of 11, 33 and 100 nM or the respective solvent control for 24h.

value: HepaRG

value: hepatocyte- and epithelial-like cells

value: 100 nM okadaic acid


title: RBG26483_Plate_4_WT


title: 100 nM OA_rep2


title: BMSC- Ta0-3


title: RBG26484_Plate_4_KO


title: RBG26486_Plate_4_KO


title: 100 nM OA_rep1


title: RBG26499_Plate_4_KO


title: RBG26498_Plate_4_KO


title: RBG26497_Plate_4_KO


title: 33 nM OA_rep3

value: 33 nM okadaic acid


title: 33 nM OA_rep2


title: RBG26501_Plate_4_KO


title: RBG26500_Plate_4_KO


title: RBG26336_Plate_3_WT


title: 33 nM OA_rep1


title: RBG26337_Plate_3_WT


title: 11 nM OA_rep3

value: 11 nM okadaic acid


title: RBG26341_Plate_3_KO


title: RBG26339_Plate_3_WT

value: WT


title: RBG26487_Plate_4_KO


title: 11 nM OA_rep1


title: solvent control_rep3

value: negative control


title: RBG26340_Plate_3_KO


title: RBG26344_Plate_3_KO


title: RBG26496_Plate_4_KO


title: RBG26345_Plate_3_KO


title: RBG26342_Plate_3_KO


title: RBG26346_Plate_3_WT


title: RBG26347_Plate_3_WT


title: 11 nM OA_rep2


title: solvent control_rep1


title: RBG26351_Plate_3_WT


title: Hs578T_washout_K27_rep2

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

institute: Nanyang Technological University

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using Bowtie2
Peaks were called using MACS2 with subtraction of input signal
bigwig files were generated using deepTools
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Breast

growth_protocol: Cell lines were seeded in DMEM + 10% FBS. After 24h, cells were starved in optimem for 8h then treated with 10ng/ml TWEAK for 48h. TWEAK was replenished after 24h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Diagenode Bioruptor. DNA was sheared to 200-500bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol

value: Breast

value: Breast Cancer

value: TWEAK+ washout


title: RBG26338_Plate_3_WT


title: RBG26321_Plate_3_KO


title: Hs578T_washout_K27_rep1


title: RBG26320_Plate_3_KO


title: liver, challenged, predicted to survive, ms23

value: liver

value: challenged, predicted to survive


title: RBG26322_Plate_3_WT


title: MB231_washout_K27_rep2


title: RBG26343_Plate_3_KO


title: MB231_washout_K27_rep1


title: RBG26323_Plate_3_WT


title: solvent control_rep2


title: RBG26324_Plate_3_WT


title: RBG26326_Plate_3_WT


title: SKBR3_TWEAK_ATAC_rep1

data_processing:
Adaptors were removed using Trimmomatic
Reads were mapped to hg38 using Bowtie2
Mitochondrial reads were removed using Bamtools
Duplicate reads were removed using Picard
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: Bed files containing called peaks

extract_protocol:
DNA was extracted by lysing cells in ATAC resuspension buffer containing NP40, TWEEN-20 and Digitonin. Followed by transposition with digitonin and Tn5 transposase
Transposed DNA was amplified through PCR with Nextera DNA CD Indexes

value: TWEAK


title: RBG26327_Plate_3_WT


title: SKBR3_TWEAK_ATAC_rep2


title: RBG26329_Plate_3_KO


title: RBG26328_Plate_3_KO


title: SKBR3_UT_ATAC_rep2

value: Untreated


title: RBG26331_Plate_3_KO

value: bone marrow


title: RBG26330_Plate_3_KO

value: ESLAM


title: RBG26349_Plate_3_WT


title: RBG26348_Plate_3_WT


title: SKBR3_UT_ATAC_rep1


title: RBG26350_Plate_3_WT


title: RBG26332_Plate_3_KO

value: KO


title: MB453_TWEAK_rep3

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using STAR
featureCounts was used to extract raw counts
Differential analysis was performed with DESeq2
Assembly: hg38
Supplementary files format and content: bed file containing raw counts

extract_protocol:
RNA was extracted using Trizol and treated with Dnase.
RNA-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol through the polyA mRNA workflow


title: RBG26307_Plate_1_KO


title: RBG26334_Plate_3_WT


title: RBG26306_Plate_1_KO


title: RBG26325_Plate_3_WT


title: RBG26305_Plate_1_KO


title: MB453_TWEAK_rep1


title: MB453_TWEAK_rep2


title: RBG26311_Plate_3_WT


title: RBG26304_Plate_1_KO


title: RBG26310_Plate_3_WT


title: RBG26309_Plate_1_KO


title: MB453_UT_rep2


title: RBG26315_Plate_3_WT


title: MB453_UT_rep1


title: RBG26308_Plate_1_KO


title: MB453_UT_rep3


title: SKBR3_TWEAK_rep3


title: SKBR3_TWEAK_rep2


title: RBG26313_Plate_3_WT


title: RBG26333_Plate_3_KO


title: RBG26312_Plate_3_WT


title: RBG26319_Plate_3_KO


title: RBG26317_Plate_3_KO


title: SKBR3_TWEAK_rep1


title: RBG26316_Plate_3_KO


title: RBG26290_Plate_1_WT


title: RBG26288_Plate_1_WT


title: SKBR3_UT_rep1


title: RBG26289_Plate_1_WT


title: RBG26335_Plate_3_WT


title: SKBR3_UT_rep2


title: RBG26291_Plate_1_WT


title: RBG26314_Plate_3_WT


title: RBG26294_Plate_1_KO


title: RBG26295_Plate_1_KO


title: MB453_input


title: MB453_TWEAK_K27_rep2


title: MB453_TWEAK_K27_rep1


title: RBG26293_Plate_1_KO


title: RBG26298_Plate_1_WT


title: MB453_UT_K27_rep2


title: RBG26299_Plate_1_WT


title: RBG26318_Plate_3_KO


title: MB453_UT_K27_rep1


title: SKBR3_UT_rep3


title: tp53 R242H/R242H, biol rep 2

city: Ottawa

first: Kim

last: Kobar

state: Ontario

address: 401 Smyth Rd

institute: Children's Hospital of Eastern Ontario Research Institute

data_processing:
MethylKit was used to filtered out regions with less than 10 reads and the highest 0.1% coverage regions as recommended and coverage was normalized between samples.
The genome was binned across in 1,000bp bins with a step size of 1,000bp and used Fisher’s Exact test to determine differentially methylated bins between the groups.
Assembly: GRCz11
Supplementary files format and content: tab-delinated text file includes filtered matrix of methylation information for regions that are covered in all samples.

organism: Danio rerio

source_name: whole larvae

growth_protocol: Larvae were maintained at 28C and samples were collected at 5 dpf.

extract_protocol:
Thirty pooled 5 dpf larvae were flash frozen, then DNA extraction andmethylation libraries were generatedusing the Post-Bisulfite Adapter Ligation method.
Starting material of 100ng of gDNA from bulk samples, one round DNA generation/random priming was used with four rounds of PCR following with a size selection step enriched for larger fragments of DNA.
Uniquely indexed libraries were pooled and submitted for sequencing on the NovaSeq6000.
Alignment and fractional methylation calls were generated using GemBS.

value: whole larvae

tag: Stage

value: 5 dpf

value: AB


title: tp53 R242H/R242H, biol rep 3


title: tp53 R242H/R242H, biol rep 1


title: tp53 R217H/R217H, biol rep 3


title: RBG26296_Plate_1_KO


title: SKBR3_input


title: tp53 R217H/R217H, biol rep 2


title: RBG26292_Plate_1_KO


title: tp53 R217H/R217H, biol rep 1


title: RBG26297_Plate_1_KO


title: SKBR3_TWEAK_K27_rep2


title: tp53 null, biol rep 3

value: tp53 null


title: RBG26302_Plate_1_WT


title: SKBR3_TWEAK_K27_rep1


title: RBG26303_Plate_1_WT


title: tp53 null, biol rep 2


title: SKBR3_UT_K27_rep1


title: RBG26301_Plate_1_WT


title: tp53 null, biol rep 1


title: SKBR3_UT_K27_rep2


title: RBG26277_Plate_1_WT


title: Hs578T_TWEAK_MAFG_rep1

value: MAFG


title: p2ry11_mutant_3

city: Tianjin

first: 林

last: 赵

state: 南开区

address: 学府街道卫津路南开大学医学协同创新中心

institute: 医学院

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software(v0.11.7)
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt(v1.17)) were aligned to reference genome(GRCh37) using Hisat2 software(v2.1.0)
The transcript abundance for each sample was estimated with StringTie(v1.3.3), and the FPKM value for gene and transcript level was calculated with R package Ballgown(v2.10.0)
Assembly: GRCh37
Supplementary files format and content: the FPKM value of detected mRNA for each sample

source_name: zebrafish larvae

growth_protocol: Larvae were kept in E3 medium with methylene blue at 28.5°C

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: zebrafish larvae

tag: time

value: 3 days post fertilization

value: p2ry11 knockout


title: RBG26276_Plate_1_WT

value: WT


title: casper, biol rep 2

value: casper


title: Hs578T_UT_MAFG_rep2

value: Breast

value: Breast Cancer


title: casper, biol rep 1


title: RBG26279_Plate_1_WT


title: Hs578T_UT_MAFG_rep1


title: RBG26278_Plate_1_WT


title: p2ry11_mutant_2

address: 学府街道卫津路南开大学医学协同创新中心


title: MB231_TWEAK_MAFG_rep2

value: TWEAK


title: p2ry11_mutant_1

address: 学府街道卫津路南开大学医学协同创新中心


title: RBG26273_Plate_1_KO


title: MB231_TWEAK_MAFG_rep1


title: WT_Sibling_Control_3

address: 学府街道卫津路南开大学医学协同创新中心


title: MB231_UT_MAFG_rep2

value: Untreated


title: RBG26275_Plate_1_WT

value: bone marrow


title: RBG26272_Plate_1_KO

value: ESLAM


title: RBG26300_Plate_1_WT


title: Hs578T_TWEAK_MAFG_rep2


title: WT_Sibling_Control_1

address: 学府街道卫津路南开大学医学协同创新中心


title: RBG26274_Plate_1_WT


title: casper, biol rep 3


title: MB231_UT_MAFG_rep1


title: MCF7_TWEAK_MAFG_rep2


title: RBG26285_Plate_1_KO

value: KO


title: rnaseh1_MO_dome_rH2AX_stacc_seq_rep2

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

data_processing:
bigWig
Supplementary files format and content: bigWig
Library strategy: stacc-seq

source_name: dome

extract_protocol: γH2AX stacc-seq was performed using anti-phospho-Histone H2A.X (Ser139) antibody (Millipore, JBW301) as described previously (Liu et al., 2020).

value: dome

value: Wild type

value: rnaseh1-MO injection


title: MCF7_TWEAK_MAFG_rep1


title: RBG26284_Plate_1_KO


title: RBG26287_Plate_1_WT


title: MCF7_UT_MAFG_rep1


title: MCF7_UT_MAFG_rep2


title: std_MO_dome_rH2AX_stacc_seq_rep1

value: std-MO injection


title: std_MO_dome_rH2AX_stacc_seq_rep2


title: rnaseh1_MO_dome_rH2AX_stacc_seq_rep1


title: RNAseq_rnaseh1MO

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (version 0.6.7).
Trimmed sequence reads were mapped to danRer7 using HISTAT2 (version 2.2.1) with default parameters.
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
BigWig files were generated by using deepTools (version 2.4.2)
danRer7
Tab-delimited text files include features' raw counts for each sample

extract_protocol:
Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer' s recommendations.


title: SKBR3_TWEAK_MAFG_rep2

value: MAFG


title: RBG26280_Plate_1_KO


title: RNAseq_StdMO

value: Std-MO injection


title: RBG26281_Plate_1_KO


title: SKBR3_UT_MAFG_rep2


title: RBG26283_Plate_1_KO


title: WT_Sibling_Control_2

address: 学府街道卫津路南开大学医学协同创新中心

value: zebrafish larvae

value: 3 days post fertilization


title: SKBR3_TWEAK_MAFG_rep1


title: RBG26282_Plate_1_KO


title: SKBR3_UT_MAFG_rep1


title: ULI-rnaseh1MO-1

data_processing:
For basic or modified ssDRIP-seq, reads were aligned to the Arabidopsis TAIR10 genome with Bowtie 2 (version 2.3.4.2) using default settings. For ULI-ssDRIP-seq without spike-in, reads were aligned to the zebrafish danRer7 genome with Bowtie 2. Duplicates were removed by Picard tools (http://broadinstitute.github.io/picard). Using samtools (version 1.3), unmapped reads and reads with more than three mismatches were removed, and the total mapped reads (non-strand R-loops) were divided into wR-loop and cR-loop reads (wR-loop means an R-loop with a Watson strand unpaired ssDNA, while cR-loop means an R-loop with a Crick strand unpaired ssDNA) . Aligned reads files (BAM) were converted to normalized coverage files (bigWig) by using deepTools (version 2.4.2). Read coverage of data from basic or modified ssDRIP-seq, or ULI-ssDRIP-seq without spike-in, was normalized to 1× sequencing depth (also known as Reads Per Genomic Content, RPGC). For quantitative ULI-ssDRIP-seq, alignment and normalization steps were different from those described above. Reads from ULI-ssDRIP-seq or input library were aligned to the zebrafish danRer7 or Arabidopsis TAIR10 genome with Bowtie 2 respectively. Normalization: First, calculated read count of ULI-ssDRIP-seq or input library mapped to danRer7 (target sample [T]) or TAIR10. (spike-in sample [S]). Tn or T(n) represented target n, while Sn or S(n) represented spike-in n (n = 1, 2, 3…, represent each sample). Choose any sample as inter-sample normalization control (represented by T1; in this study, muscle rep1 was chosen as T1), and calculated its normalization factor of reads mapped to danRer7 in RPGC manner described above. T(n)R-loop represented read count of ULI-ssDRIP-seq library from T(n) mapped to danRer7, while S(n)input represented read count of input library from S(n) mapped to TAIR10. By analogy, T(n)input represented read count of input library from T(n) mapped to danRer7, while S(n)R-loop represented read count of ULI-ssDRIP-seq library from S(n) mapped to TAIR10. The quantitative factor of Tn equaled [T(n)R-loop × S(n)input] / [ S(n)R-loop × T(n)input]. The finial normalization factor of Tn equaled Quantitative factor (Tn) multiplied by Normalization factor (T1) divided by Quantitative factor (T1). For other samples except T1, the finial normalization factor was used for normalization to convert bigWig file.
bigWig

extract_protocol: Samples collected were lysed in genome extraction buffer (200 mM NaCl, 10 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% SDS, 200 μg /ml freshly added Proteinase K) at 37°C for 8~12 h. Then, 1/4 volume of 5 M potassium acetate solution (pH 5.2) was added to the lysate and mixed gently, followed by incubation on ice for 20 min. Following extraction with equal volume of phenol: chloroform: isoamyl alcohol (25:24:1, pH 7.8) and chloroform sequentially with phase-lock tubes. The supernatant containing genomic DNA was precipitated by addition of equal volume of isopropanol and 1 μl GlycoBlue (Thermo Fisher) for 30 min at -20°C. The precipitate was washed by 70% ethanol for once and then air-dried.  Genomic DNA was digested with mung bean nuclease (TaKaRa) at 37°C for 2 h and purified by the phenol-chloroform method followed by resuspending the pellet in 130 μl TE buffer. Digested gDNA was sonicated to a peak fragment size of 250 bp, performed on a S220 Focused-ultrasonicator with 10% Duty Factor, 200 cycles/burst, 175 peak incident power and for 90 sec per tube. For inter-group relative quantification, gDNA from Arabidopsis (7-day-old Col-0 seedlings) was used as the spike-in sample to normalize total R-loop levels between animal samples. Sonicated spike-in gDNA to a peak fragment size of 250 bp as described above, and then added ~0.1 ng sonicated spike-in gDNA to sonicated target gDNA samples. 80% of the mixed sample was used for the first adapter ligation of ULI-ssDRIP-seq workflow, and the rest 20% part was used for input-library preparation by using Accel-NGS 1S Plus DNA Library Kit following the manual. For the first adapter ligation (pre-ligation), 53 μl sonicated gDNA was added to Adaptase reaction mix (for each sample: 8 μl buffer G1, 8 μl reagent G2, 5 μl reagent G3, 2 μl enzyme G4, 2 μl enzyme G5, and 2 μl enzyme G6, from Accel-NGS 1S Plus DNA Library Kit), incubated at 37°C for 1 hour. Then DRIP was performed as described previously 5. Prepared 174 ul pre-mixed extension reaction mix following the extension part of manual (Accel-NGS 1S Plus DNA Library Kit) and mixed with beads/antibody complexes, followed by 1 cycle PCR (98°C 90 sec, 63°C 30 sec, 68°C 5 min). Purified DNA by adding 1.2 volumes of SPRIselect beads. Ligated the second truncated adapter to the 5’ ends at 25°C for 1 hour following the ligation part of manual (Accel-NGS 1S Plus DNA Library Kit). Purified DNA again by 1 volume SPRIselect beads and eluted with 21 ul Low EDTA buffer. 1 ul purified DNA was used for qPCR by using indexing primers to address cycle numbers of indexing PCR. The cycle numbers of indexing PCR was equal to the Ct value. An indexing PCR step was performed following the manual of Accel-NGS® 1S Plus DNA Library Kit.


title: ULI-rnaseh1MO-2


title: RBG26260_Plate_1_KO


title: Hs578T_Fn14KO_K27_TW2


title: ULI-stdMO-2


title: Hs578T_Fn14KO_K27_TW1


title: RBG26261_Plate_1_KO


title: ULI-stdMO-1


title: Hs578T_Fn14KO_K27_UT2


title: RBG26286_Plate_1_WT

value: WT


title: RBG26262_Plate_1_WT


title: ULI-RNH-dome-2

value: hRNaseH1 injection


title: Hs578T_Fn14KO_K27_UT1

value: Breast


title: RBG26256_Plate_1_KO


title: Hs578T_control_K27_TW2

value: Breast Cancer


title: RBG26263_Plate_1_WT


title: ULI-GFP-dome-2

value: GFP injection


title: Hs578T_control_K27_TW1

value: TWEAK


title: RBG26257_Plate_1_KO

value: bone marrow


title: ULI-GFP-dome-1


title: Hs578T_control_K27_UT2

value: Untreated


title: Hs578T_control_K27_UT1


title: RBG26259_Plate_1_KO

value: ESLAM

value: KO


title: Pol_II_ChIPseq_GFP

data_processing:
For Pol II ChIP-seq data analysis, reads were aligned to the zebrafish danRer7 genome with Bowtie 2 to get alignment files (SAM). Then, SAM files were converted to BAM files following sorting and indexing with samtools (Li et al., 2009) (version 1.3). Duplicates were removed by Picard tools (http://broadinstitute.github.io/picard). For visualization, aligned reads were converted to normalized coverage files (bigWig) by using bamCoverage from deepTools (Ramirez et al., 2014) (version 2.4.2). To compare enrichment of Pol II signal in genes among samples, raw counts for the feature of genes were extracted by FeatureCounts (Liao et al., 2014) (version 2.0.3) and differential Pol II enriched genes were analyzed by using R package NOISeq (version 3.17) according to the user's guide (Tarazona et al., 2015).
bigWig

extract_protocol: 100 embryos at dome stage were collected for each sample and fixed in cross-linking buffer (50mM HEPES pH8.0, 0.1 M NaCl, 1 mM EDTA, 0.5 M EGTA, 1 % Formaldehyde) for 15 min at room temperature. For chromatin fragmentation, 400 μl ChIP lysis buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 0.1 % Sodium Deoxycholate, 1% Triton-X) with 1 × PIC and 1 mM PMSF were added to fixed embryos and incubated in ice for 20 min. Then, sonication was performed on ME220 with 10% duty factor, 75 peak incident power, 1000 cycles/burst, and for 600 second per tube. Fragmented chromatins were centrifuged at 12,000 rpm for 10 min at 4°C to remove cellular debris. For IP, 2 μg RNA Pol II antibody (Active Motif, no. 61667) and 10 μl Dynabeads™ Protein G were added to the fragmented chromatin solution and incubated at 4°C overnight with rotator at speed of 10 rpm. Beads containing immuno-bound chromatin were collected by placing the microfuge tube on a magnet rack and washed with ChIP lysis buffe 2 times, High salt wash buffer (10 mM Tris, pH 8.0, 500 mM NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % SDS, and 0.1% Sodium Deoxycholate) 2 times, LiCl wash buffer (10 mM Tris, pH 8.0, 250mM LiCl, 1 mM EDTA, 1 % Triton-X, 0.5 % SDS, and 0.5% Sodium Deoxycholate) 1 time, and TE 2 times, mixing 5 minutes for each wash on a rotator at 4°C. Then, the beads were suspended in 200 μl IP Elution Buffer with 200 μg/ml Proteinase K and incubated at 65°C overnight for reverse cross-linking, following DNA extraction with an equal volume of phenol: chloroform: isoamyl alcohol (25:24:1, pH 7.8) with phase-lock tubes. The supernatant containing ChIP DNA was precipitated by addition of an equal volume of isopropanol and 1 μl GlycoBlue (Thermo Fisher) for 12 h at -20°C. Accel-NGS 1S Plus DNA Library Kit was used for library construction following the manual.

value: dome

value: Wild type


title: Pol_II_ChIPseq_hRNaseH1GFP


title: RBG26268_Plate_1_KO


title: Zebrafish, hRNaseH1, dome, RNA-seq, Rep1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (version 0.6.7).
Trimmed sequence reads were mapped to danRer7 using HISTAT2 (version 2.2.1) with default parameters.
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
BigWig files were generated by using deepTools (version 2.4.2)
Assembly: danRer7
Supplementary files format and content: bw


title: MB231_Fn14KO_K27_TW2


title: MB231_Fn14KO_K27_UT2


title: MB231_Fn14KO_K27_TW1


title: RBG26270_Plate_1_KO


title: Zebrafish, GFP, dome, RNA-seq, Rep2


title: RBG26269_Plate_1_KO


title: MB231_Fn14KO_K27_UT1


title: Zebrafish, GFP, dome, RNA-seq, Rep1


title: RBG26271_Plate_1_KO


title: MB231_control_K27_TW2


title: ULI-RNH-dome-1


title: RBG26264_Plate_1_WT


title: MB231_control_K27_TW1


title: RBG26265_Plate_1_WT


title: MB231_control_K27_UT2


title: Zebrafish, Input_Muscle1

data_processing:
Library strategy: DRIP-seq
For basic or modified ssDRIP-seq, reads were aligned to the Arabidopsis TAIR10 genome with Bowtie 2  (version 2.3.4.2) using default settings. For ULI-ssDRIP-seq without spike-in, reads were aligned to the zebrafish danRer7 genome with Bowtie 2. Duplicates were removed by Picard tools (http://broadinstitute.github.io/picard). Using samtools (version 1.3), unmapped reads and reads with more than three mismatches were removed, and the total mapped reads (non-strand R-loops) were divided into wR-loop and cR-loop reads (wR-loop means an R-loop with a Watson strand unpaired ssDNA, while cR-loop means an R-loop with a Crick strand unpaired ssDNA) . Aligned reads files (BAM) were converted to normalized coverage files (bigWig) by using deepTools (version 2.4.2). Read coverage of data from basic or modified ssDRIP-seq, or ULI-ssDRIP-seq without spike-in, was normalized to 1× sequencing depth (also known as Reads Per Genomic Content, RPGC). For quantitative ULI-ssDRIP-seq, alignment and normalization steps were different from those described above. Reads from ULI-ssDRIP-seq or input library were aligned to the zebrafish danRer7 or Arabidopsis TAIR10 genome with Bowtie 2 respectively. Normalization: First, calculated read count of ULI-ssDRIP-seq or input library mapped to danRer7 (target sample [T]) or TAIR10. (spike-in sample [S]). Tn or T(n) represented target n, while Sn or S(n) represented spike-in n (n = 1, 2, 3…, represent each sample). Choose any sample as inter-sample normalization control (represented by T1; in this study, muscle rep1 was chosen as T1), and calculated its normalization factor of reads mapped to danRer7 in RPGC manner described above. T(n)R-loop represented read count of ULI-ssDRIP-seq library from T(n) mapped to danRer7, while S(n)input represented read count of input library from S(n) mapped to TAIR10. By analogy, T(n)input represented read count of input library from T(n) mapped to danRer7, while S(n)R-loop represented read count of ULI-ssDRIP-seq library from S(n) mapped to TAIR10. The quantitative factor of Tn equaled [T(n)R-loop × S(n)input] / [ S(n)R-loop × T(n)input]. The finial normalization factor of Tn equaled Quantitative factor (Tn) multiplied by Normalization factor (T1) divided by Quantitative factor (T1). For other samples except T1, the finial normalization factor was used for normalization to convert bigWig file.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

source_name: muscle

extract_protocol:
Samples collected were lysed in genome extraction buffer (200 mM NaCl, 10 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% SDS, 200 μg /ml freshly added Proteinase K) at 37°C for 8~12 h. Then, 1/4 volume of 5 M potassium acetate solution (pH 5.2) was added to the lysate and mixed gently, followed by incubation on ice for 20 min. Following extraction with equal volume of phenol: chloroform: isoamyl alcohol (25:24:1, pH 7.8) and chloroform sequentially with phase-lock tubes. The supernatant containing genomic DNA was precipitated by addition of equal volume of isopropanol and 1 μl GlycoBlue (Thermo Fisher) for 30 min at -20°C. The precipitate was washed by 70% ethanol for once and then air-dried.
Genomic DNA was digested with mung bean nuclease (TaKaRa) at 37°C for 2 h and purified by the phenol-chloroform method followed by resuspending the pellet in 130 μl TE buffer. Digested gDNA was sonicated to a peak fragment size of 250 bp, performed on a S220 Focused-ultrasonicator with 10% Duty Factor, 200 cycles/burst, 175 peak incident power and for 90 sec per tube. For inter-group relative quantification, gDNA from Arabidopsis (7-day-old Col-0 seedlings) was used as the spike-in sample to normalize total R-loop levels between animal samples. Sonicated spike-in gDNA to a peak fragment size of 250 bp as described above, and then added ~0.1 ng sonicated spike-in gDNA to sonicated target gDNA samples. 80% of the mixed sample was used for the first adapter ligation of ULI-ssDRIP-seq workflow, and the rest 20% part was used for input-library preparation by using Accel-NGS 1S Plus DNA Library Kit following the manual. For the first adapter ligation (pre-ligation), 53 μl sonicated gDNA was added to Adaptase reaction mix (for each sample: 8 μl buffer G1, 8 μl reagent G2, 5 μl reagent G3, 2 μl enzyme G4, 2 μl enzyme G5, and 2 μl enzyme G6, from Accel-NGS 1S Plus DNA Library Kit), incubated at 37°C for 1 hour. Then DRIP was performed as described previously 5. Prepared 174 ul pre-mixed extension reaction mix following the extension part of manual (Accel-NGS 1S Plus DNA Library Kit) and mixed with beads/antibody complexes, followed by 1 cycle PCR (98°C 90 sec, 63°C 30 sec, 68°C 5 min). Purified DNA by adding 1.2 volumes of SPRIselect beads. Ligated the second truncated adapter to the 5’ ends at 25°C for 1 hour following the ligation part of manual (Accel-NGS 1S Plus DNA Library Kit). Purified DNA again by 1 volume SPRIselect beads and eluted with 21 ul Low EDTA buffer. 1 ul purified DNA was used for qPCR by using indexing primers to address cycle numbers of indexing PCR. The cycle numbers of indexing PCR was equal to the Ct value. An indexing PCR step was performed following the manual of Accel-NGS® 1S Plus DNA Library Kit.

tag: ecotype

value: Tubingen

tag: developmental stage

value: muscle

tag: pulldown of

value: DNA:RNA hybrid

tag: protocol

value: Input library of ULI-ssDRIP-seq with spike-in


title: RBG26258_Plate_1_KO

tag: tissue

tag: cell type


title: Zebrafish, Input_Muscle2

tag: genotype


title: Zebrafish, Input_Dome2

source_name: dome stage embryos

value: dome stage embryos


title: RBG26247_Plate_1_KO


title: RBG26267_Plate_1_WT

value: WT


title: HL-7702 cells, Ensartinib Treatment, 24h, rep3

city: Hangzhou

first: Wu

middle: Wen

last: Tong

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: HL-7702 cells were maintained in 1640 supplymented with 10% fetal bovine serum（FBS）and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: HL-7702 cells were treated DMSO or 2μM Ensartinib for 24h.

value: Human hepatocyte

value: Ensartinib 2μM，24h


title: Zebrafish, Input_256Cell2

source_name: 256-cell stage embryos

value: 256-cell stage embryos


title: Zebrafish, Input_Dome1


title: MB231_control_K27_UT1

value: Breast

value: Breast Cancer


title: HL-7702 cells, Ensartinib Treatment, 24h, rep2


title: RBG26246_Plate_1_KO

value: bone marrow


title: Zebrafish, Input_256Cell1


title: Zebrafish, hRNaseH1, dome, RNA-seq, Rep2

value: hRNaseH1 injection


title: HL-7702 cells, Ensartinib Treatment, 24h, rep1


title: Zebrafish, Input_4Cell2

source_name: 4-cell stage embryos

value: 4-cell stage embryos


title: RBG26245_Plate_1_KO

value: ESLAM

value: KO


title: HL-7702 cells, DMSO Treatment, 24h, rep2

value: DMSO


title: RBG26244_Plate_1_KO


title: Zebrafish, Input_4Cell1

value: Wild type

value: Tubingen


title: RBG26243_Plate_1_WT


title: HL-7702 cells, DMSO Treatment, 24h, rep1


title: RBG26266_Plate_1_WT


title: Zebrafish, Input_Sperm2

source_name: sperm

value: sperm

value: DNA:RNA hybrid


title: RBG26242_Plate_1_WT


title: RBG26241_Plate_1_WT


title: Zebrafish, Input_Sperm1

value: Input library of ULI-ssDRIP-seq with spike-in


title: VEGF

city: Chongqing

first: Wei

last: Fan

address: Youyi Road, No1

department: Urology

institute: The First affiliated hospital of Chongqing Medical University

data_processing:
*library strategy: CUT& Tag
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. The library preparations were sequenced on Illumina Novaseq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd. (Beijing, China) and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.0). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v0.7.12) and clean reads were aligned to the reference genome using BWA mem  -k 32 -T 30 -t 4 -M. These reads were then filtered for high quality (MAPQ ≥ 13), we also removed reads that were not properly paired and with PCR duplicates. Only uniquely mapped(MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
All peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER( v4.9.1) software with ‘-len 8,10,12,14 -gc -size given -homer2 -dumpFasta’.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker (Yu et al., 2015) was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak-related gene. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: retina

growth_protocol: HRMECs were purchased from Cell Systems (ACBRI 181, Seattle, America) and cultured in Complete Classic Medium with Serum & Culture Boost (4Z0-500, Cell Systems) at 37°C under 5% CO2.

extract_protocol:
The cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation.
DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPure beads.

treatment_protocol: HRMECs were treated with 0 or 100 ng/ml VEGF for 24 h (Control and VEGF group respectively)

value: retina

value: HRMEC

value: endothelial cells

value: WT

value: 100 ng/ml VEGF


title: Zebrafish, Input_Oocyte2

source_name: oocyte

value: oocyte


title: RBG26240_Plate_1_WT

value: bone marrow


title: Zebrafish, Input_Oocyte1


title: Control

value: 0 ng/ml VEGF


title: RBG26255_Plate_1_WT


title: RBG26254_Plate_1_WT


title: Flp-In 293 T-REx, CLIP-UPF1 LECY, siUPF1, rep3

city: Bethesda

first: J. Robert

last: Hogg

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

data_processing:
FASTQ files were trimmed to remove TruSeq adapter sequences and quality filtered using Cutadapt.
Trimmed reads were subjected to two-pass STAR alignment.
Gene-level transcript abundance was determined using RSEM quantification against Gencode transcript annotations. Gene counts were passed through a CPM filter of 0.5 and subjected to differential expression analysis using DESeq2.
The BAM files resulting from the two-pass STAR alignment to the human genome were used as inputs into rMATS 4.1.0 software for junction-level analysis.
Assembly: hg38
Supplementary files format and content: Tab-delimited file contains gene-level expected counts, as determined by RSEM quantification..

source_name: Flp-In 293 T-REx cell line

growth_protocol: Flp-In 293 T-REx cell lines were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , 0.3 mg/ml L-glutamine, and 100 µg/mL Hygromycin B (Invitrogen) at 37°C and 5% CO2.

extract_protocol:
RNA was purified using the TRIzol Reagent (Invitrogen), treated with Shrimp dsDNase (Thermo Scientific), and cleaned up with RNAclean XP beads.
500 ng of total RNA was used per sample for library preparation. Ribosomal RNA was depleted using antisense rRNA oligonucleotides and thermostable RNase H, and libraries were generated using the xGen™ RNA Library Preparation Kit (IDT)

treatment_protocol: Flp-In 293 T-REx cell lines stably expressing a CLIP-UPF1 mutant were reverse-transfected with 40 nM of the indicated siRNA using Lipofectamine RNAiMAX at a seed density of 300,000 in 6-well plates (without Hygromycin B), and RNA was harvested 72 hrs post-transfection.

value: Flp-In 293 T-REx cell line

value: UPF1 siRNA


title: Flp-In 293 T-REx, CLIP-UPF1 LECY, siNT, rep3

value: non-targeting siRNA


title: Zebrafish, Muscle2

value: muscle

value: ULI-ssDRIP-seq with spike-in


title: Zebrafish, Muscle1

value: Wild type

value: Tubingen


title: Zebrafish, Dome2

value: dome stage embryos

value: DNA:RNA hybrid


title: RBG26253_Plate_1_WT

value: ESLAM


title: HL-7702 cells, DMSO Treatment, 24h, rep3

value: Human hepatocyte

value: DMSO


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siNT, rep3


title: RBG26252_Plate_1_WT

value: WT


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siUPF1, rep3


title: Zebrafish, Dome1


title: Flp-In 293 T-REx, CLIP-UPF1 IR-ER, siUPF1, rep3


title: Zebrafish, 256Cell2

value: 256-cell stage embryos


title: RBG26251_Plate_1_WT


title: Flp-In 293 T-REx, CLIP-UPF1 IR-ER, siNT, rep3


title: Flp-In 293 T-REx, CLIP-UPF1 I757R, siUPF1, rep3


title: RBG26249_Plate_1_KO

value: KO


title: RBG26250_Plate_1_WT

value: bone marrow


title: Zebrafish, 256Cell1


title: Flp-In 293 T-REx, CLIP-UPF1 I757R, siNT, rep3


title: Zebrafish, 4Cell1

value: 4-cell stage embryos


title: Zebrafish, 4Cell2


title: RBG26248_Plate_1_KO


title: Flp-In 293 T-REx, CLIP-UPF1 FE-ER, siUPF1, rep3

value: Flp-In 293 T-REx cell line


title: RBG26230_Plate_1_WT


title: Flp-In 293 T-REx, CLIP-UPF1 FE-ER, siNT, rep3


title: Zebrafish, Sperm2

value: sperm


title: Zebrafish, Sperm1


title: Flp-In 293 T-REx, CLIP-UPF1 F192E, siUPF1, rep3

value: UPF1 siRNA


title: Zebrafish, Oocyte2

value: oocyte


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siNT, rep3

value: non-targeting siRNA


title: Flp-In 293 T-REx, CLIP-UPF1 F192E, siNT, rep3


title: Zebrafish, 500kc_ssDRIP_seq

value: Wild type

value: muscle

value: Basic ssDRIP-seq


title: RBG26227_Plate_1_WT


title: RBG26229_Plate_1_WT


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siUPF1, rep3


title: Zebrafish, RNaseH

value: Tubingen

value: DNA:RNA hybrid

value: ULI-ssDRIP-seq without spike-in, negative control by RNase H treatment


title: Zebrafish, Oocyte1

value: ULI-ssDRIP-seq with spike-in


title: Flp-In 293 T-REx, CLIP, siUPF1, rep3


title: Zebrafish, 10kc

value: ULI-ssDRIP-seq without spike-in


title: Zebrafish, 1kc


title: RBG26231_Plate_1_WT

value: ESLAM

value: WT


title: Flp-In 293 T-REx, CLIP-UPF1 LECY, siUPF1, rep2


title: RBG26238_Plate_1_WT

value: bone marrow


title: RBG26228_Plate_1_WT


title: Flp-In 293 T-REx, CLIP-UPF1 LECY, siNT, rep2


title: Flp-In 293 T-REx, CLIP, siNT, rep3


title: Zebrafish, 100c


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siUPF1, rep2


title: Zebrafish, 10c


title: Arabidopsis thaliana, dsD_ssDRIP_seq

organism: Arabidopsis thaliana

source_name: seedlings

value: Columbia

value: seedlings

value: Modified ssDRIP-seq by dsDNase treatment


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siNT, rep2

value: Flp-In 293 T-REx cell line


title: RBG26236_Plate_1_KO

value: KO


title: RBG26226_Plate_1_WT


title: RBG26239_Plate_1_WT


title: RBG26237_Plate_1_KO


title: RBG26224_Plate_1_KO


title: Arabidopsis thaliana, MBN_ssDRIP_seq

value: Modified ssDRIP-seq by mung bean nucelase treatment


title: RBG26232_Plate_1_KO


title: Arabidopsis thaliana, RE_ssDRIP_seq

value: Wild type

value: Baisc ssDRIP-seq by restriction enzyme treatment


title: RBG26234_Plate_1_KO


title: Flp-In 293 T-REx, CLIP-UPF1 IR-ER, siUPF1, rep2

value: UPF1 siRNA


title: Arabidopsis thaliana, S1_ssDRIP_seq

value: Modified ssDRIP-seq by S1 nucelase treatment


title: RBG26225_Plate_1_KO


title: Flp-In 293 T-REx, CLIP-UPF1 I757R, siUPF1, rep2


title: RBG26235_Plate_1_KO


title: RBG26233_Plate_1_KO


title: Flp-In 293 T-REx, CLIP-UPF1 I757R, siNT, rep2

value: non-targeting siRNA


city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
H9 hESC-differentiated Schwann cells replicate 3
H9_SC_Pass2_3

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to GRCh38 using STAR spliced read aligner
Count read using HT-seq with GRCh38 as reference
Normalization (TMM), quantitation,  and differential expression analysis using egdeR.
Assembly: GRCh38
Supplementary files format and content: Counts

source_name: Schwann cells

growth_protocol: hESC and hiPSCs were cultured using standard protocols. Cells were differentiated and purified as described previously (Mukherjee-Clavin, B., Mi, R., Kern, B., Choi, I.Y., Lim, H., Oh, Y., Lannon, B., Kim, K.J., Bell, S., Hur, J.K., et al. (2019). Comparison of three congruent patient-specific cell types for the modelling of a human genetic Schwann-cell disorder. Nat Biomed Eng 3, 571-582. 10.1038/s41551-019-0381-8).

extract_protocol:
RNA was isolated from hESC- and iPSC-derived Schwann cells at passage two with TRIzol (Thermo Fisher Scientific) following the manufacturer’s protocol and subsequent purification with a RNeasy Mini Kit (Qiagen). RNA quality was verified with a bioanalyzer.
Library was prepared using Illumina TruSeq Stranded RNA (100 ng).
RNA-sequencing was carried out using TrueSeq RiboZero gold (stranded) kit (Illumina).

value: Schwann cells

value: hESC

value: Healthy Control


title: Arabidopsis thaliana, dsF_ssDRIP_seq

value: DNA:RNA hybrid

value: Modified ssDRIP-seq by dsDNA Fragmentase treatment


title: RBG26472_Plate_4_KO

data_processing:
RNA-seq reads were aligned to mm10 + ERCC92 using GSNAP (version 2018-03-25) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.9.1) with the parameter (-s no).
Assembly: GRCm38.81
Supplementary files format and content: HTSeq counts text file with raw counts and htseq metrics
Supplementary files format and content: Anndata h5 file with filtered cells and genes and data transformations (in layers)

value: bone marrow

value: ESLAM


title: Flp-In 293 T-REx, CLIP-UPF1 FE-ER, siUPF1, rep2


title: Flp-In 293 T-REx, CLIP-UPF1 FE-ER, siNT, rep2


description:
H9 hESC-differentiated Schwann cells replicate 1
H9_SC_Pass2_1


title: Flp-In 293 T-REx, CLIP-UPF1 F192E, siUPF1, rep2


title: RBG26475_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 F192E, siNT, rep2


title: Flp-In 293 T-REx, CLIP-UPF1 IR-ER, siNT, rep2


description:
hiPSC-differentiated Schwann cells replicate 2
2ipsc_scP2_25_3

value: hiPSC


title: RBG26476_Plate_4_KO


title: RBG26474_Plate_4_KO


description:
hiPSC-differentiated Schwann cells replicate 1
2ipsc_scP2_25_1


title: HMLE cells, DMSO, hnRNPM iCLIP, biol rep 2

city: Houston

first: Chonghui

last: Cheng

state: TX

address: 1 Baylor Plaza

department: Breast Center

institute: Baylor College of Medicine

data_processing:
Data analysis was conducted using the Clip Tool Kit (CTK) v1.0.3 after processing and mapping iCLIP reads in CTK, replicates were pooled and single nucleotide resolution binding sites for hnRNPM were determined using the following strategy: 1) Statistically significant iCLIP peaks were called and delimited by one half the peak height (adjusted p<0.05); 2) Significant crosslinking induced truncation sites (CITS) were called (adjusted p<0.05) using the CTK CITS.pl script; 3) CITS were further filtered by retaining only those that overlapped with a significant peak; 4) CITS were extended upstream and downstream by 10 nucleotides to identify local binding sites for further analysis
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include significant hnRNPM binding peaks information

source_name: HMLE

growth_protocol: HMLE cells were grown in Mammary Epithelial Cell Growth Medium (Lonza, USA)

extract_protocol:
performed using anti-hnRNPM antibody (Origene)
iCLIP libraries were sent for sequencing

treatment_protocol: UV crosslinked

value: HMLE

value: breast epithelial cells

value: WT

tag: antibody

value: anti-hnRNPM


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siUPF1, rep2

tag: cell line

value: Flp-In 293 T-REx cell line


title: HMLE cells, DMSO, hnRNPM iCLIP, biol rep 1


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siNT, rep2


title: RBG26478_Plate_4_WT

source_name: bone marrow

extract_protocol:
Bone marrow cells were harvested from STAT5KO and WT control mice, single ESLAM HSCs was FACS sorted into 2.3ul 0.2% Triton-100 containg RNAse inhibitor
Tagmentation is carried out using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm.


title: Flp-In 293 T-REx, CLIP, siNT, rep2


title: Flp-In 293 T-REx, CLIP, siUPF1, rep2


title: RBG26479_Plate_4_WT


title: HMLE cells, shhnRNPM, biol rep 3

data_processing:
RNA-seq reads were aligned to the human genome (GRCh37, primary assembly) and transcriptome (Gencode version 24 backmap 37 comprehensive gene annotation) using STAR v2.7.9a with the following non-standard parameters --outSAMstrandField intronMotif --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 --alignEndsType EndToEnd. Only uniquely aligned reads were retained for downstream analysis
Read count extraction were performed using featureCounts version 1.5.0 with the following non-default parameters -s 0 -a and later fpkm normalized
Differential gene expression analysis was conducted using DESeq2 performed on genes with at least 5 counts present in at least half of the samples
Alternative splicing of skipped exons was quantified using rMATS version 4.0.2 with the following non-default parameters -readLength 100 -cstat 0.01 -libType fr-secondstrand
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include fpkm normalized gene expression information for each sample and log2 fold changes of genes between control and hnRNPM knockdown in HMLE cells
Supplementary files format and content: Tab-delimited text files include alternative splicing information for each sample

growth_protocol: HMLE cells were grown in Mammary Epithelial Cell Growth Medium (Lonza, USA), and HeLa, LM2 and BM2 cells were grown in DMEM supplemented with 10% FBS, L-glutamine and Pen/Strep at 37 degrees.

extract_protocol:
RNA samples were extracted following by the TRIzol Reagent kit from Invitrogen
The purified RNA samples were submitted to the Genomic Facility at University of Chicago for RNA quality validation, RNA-seq library generation and paired-end sequencing on HiSeq 4000

treatment_protocol: hnRNPM siRNA knockdown was performed using Lipofectamine RNAiMAX reagent (Invitrogen)

value: hnRNPM knockdown


title: RBG26464_Plate_4_KO

value: KO


title: Flp-In 293 T-REx, CLIP-UPF1 LECY, siNT, rep1


title: Flp-In 293 T-REx, CLIP-UPF1 LECY, siUPF1, rep1

value: UPF1 siRNA


title: RBG26465_Plate_4_KO


description:
H9 hESC-differentiated Schwann cells replicate 2
H9_SC_Pass2_2

tag: condition


title: RBG26473_Plate_4_KO


description:
hiPSC-differentiated Schwann cells replicate 3
2ipsc_scP2_29_1


title: HMLE cells, shhnRNPM, biol rep 2


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siUPF1, rep1


title: RBG26477_Plate_4_KO


title: RBG26467_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 IR-ER, siUPF1, rep1


title: HMLE cells, shControl, biol rep 2


title: HMLE cells, shhnRNPM, biol rep 1


title: RBG26468_Plate_4_WT


title: HMLE cells, shControl, biol rep 1


title: Flp-In 293 T-REx, CLIP-UPF1 IR-ER, siNT, rep1

value: non-targeting siRNA


title: RBG26469_Plate_4_WT


title: H9 hESC-differentiated Schwann cells

description: H9 hESC-differentiated Schwann cells

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to GRCh38 using STAR spliced read aligner
Count read using HT-seq with GRCh38 as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using egdeR.
Assembly: GRCh38
Supplementary files format and content: Counts

source_name: H9 hESC-differentiated Schwann cells

extract_protocol:
RNA was isolated from hESC- and iPSC-derived Schwann cells at passage two with TRIzol (Thermo Fisher Scientific) following the manufacturer’s protocol and subsequent purification with a RNeasy Mini Kit (Qiagen). RNA quality was verified with a bioanalyzer.
Library was prepared using Illumina TruSeq Stranded RNA (100 ng).

value: Healthy Control (female embryo)

value: Differentiated Schwann cells

value: H9 hESC


title: H7 hESC-differentiated Schwann cells

description: H7 hESC-differentiated Schwann cells

source_name: H7 hESC-differentiated Schwann cells

value: H7 hESC


title: Flp-In 293 T-REx, CLIP-UPF1 I757R, siUPF1, rep1


title: Flp-In 293 T-REx, CLIP-UPF1 I757R, siNT, rep1


title: RBG26470_Plate_4_WT


title: HMLE cells, shControl, biol rep 3


title: RBG26471_Plate_4_WT


title: RBG26457_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 FE-ER, siNT, rep1


title: GM08398 hiPSC-differentiated Schwann cells

value: Healthy Control (8YO male donor)

value: GM08398 hiPSC


title: GM02623 hiPSC-differentiated Schwann cells

value: Healthy Control (61YO female donor)

value: GM02623 hiPSC


title: RBG26456_Plate_4_WT

value: bone marrow

value: ESLAM


title: Flp-In 293 T-REx, CLIP-UPF1 F192E, siUPF1, rep1


title: RBG26466_Plate_4_WT

value: WT


title: RBG26459_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siNT, rep1


title: GM01582 hiPSC-differentiated Schwann cells

value: Healthy Control (11YO female donor)

value: GM01582 hiPSC


title: RBG26458_Plate_4_WT


title: Gclc KO 4 Batch 2-2

city: Rochester

first: Isaac

middle: Spencer

last: Harris

state: New York

address: 601 Elmwood Ave

department: Department of Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Demultiplexing software version: bcl2fastq2 v2.2.
Differential expression and GSEA analyses were performed as previously described1,2.
References:
1. Frazee, A. C. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol 33, 243-246 (2015). https://doi.org/10.1038/nbt.3172
2. Korotkevich, G. et al. Fast gene set enrichment analysis. bioRxiv, 060012 (2021). https://doi.org/10.1101/060012
Assembly: Mus musculus
Supplementary files format and content: Excel file with normalized counts.

source_name: Liver

growth_protocol: Gclc f/f and Gclc f/f Rosa26-CreERT2 mice were treated with tamoxifen (i.p., 150 mg/kg, 5 days). After 14 days, mice were sacrifice and the liver was harvested.

extract_protocol:
RNA extracted using Invitrogen PureLink RNA Mini Kit
RNA libraries for RNA-seq were prepared using Kapa mRNA Directional Library Preparation following manufacturers protocols.

value: Liver

value: Gclc KO


title: Gclc KO 4 Batch 1-2


title: Flp-In 293 T-REx, CLIP-UPF1 F192E, siNT, rep1

value: Flp-In 293 T-REx cell line


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siNT, rep1

value: non-targeting siRNA


title: RBG26463_Plate_4_KO

value: KO


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siUPF1, rep1

value: UPF1 siRNA


title: Flp-In 293 T-REx, CLIP, siUPF1, rep1


title: RBG26462_Plate_4_KO


title: Flp-In 293 T-REx, CLIP, siNT, rep1


title: Gclc WT 4 Batch 2-2

value: Gclc WT


title: H1 hESC-differentiated Schwann cells

description: H1 hESC-differentiated Schwann cells

source_name: H1 hESC-differentiated Schwann cells

value: Healthy Control (male embryo)

value: Differentiated Schwann cells

value: H1 hESC


title: Flp-In 293 T-REx, CLIP-UPF1 FE-ER, siUPF1, rep1


title: RBG26460_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siUPF1, rep 2

data_processing:
FASTQ files were trimmed to remove TruSeq adapter sequences and quality filtered using Cutadapt.
Trimmed reads were subjected to two-pass STAR alignment.
Gene-level transcript abundance was determined using RSEM quantification against Gencode transcript annotations. Gene counts were passed through a CPM filter of 0.5 and subjected to differential expression analysis using DESeq2.
The BAM files resulting from the two-pass STAR alignment to the human genome were used as inputs into rMATS 4.1.0 software for junction-level analysis.
Assembly: hg19
Supplementary files format and content: Tab-delimited file contains gene-level expected counts, as determined by RSEM quantification..


title: RBG26449_Plate_4_KO


title: RBG26448_Plate_4_KO


title: Gclc WT 4 Batch 2-1


title: Gclc WT 4 Batch 1-2


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siUPF1, rep 1


title: RBG26451_Plate_4_KO


title: RBG26461_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siNT, rep 3


title: Gclc KO 4 Batch 2-1


title: RBG26450_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siNT, rep 2


title: RBG26453_Plate_4_KO


title: Gclc KO 3 Batch 2-2


title: Gclc KO 4 Batch 1-1


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siUPF1, rep 3


title: Flp-In 293 T-REx, CLIP-UPF1 WT, siNT, rep 1


title: Flp-In 293 T-REx, CLIP-UPF1 R843C, siUPF1, rep 3


title: RBG26452_Plate_4_KO


title: Gclc KO 3 Batch 2-1


title: Gclc KO 3 Batch 1-1


title: Flp-In 293 T-REx, CLIP-UPF1 R843C, siUPF1, rep 2


title: RBG26454_Plate_4_WT


title: RBG26455_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 R843C, siUPF1, rep 1


title: Gclc WT 3 Batch 2-2


title: Gclc WT 4 Batch 1-1


title: Gclc WT 3 Batch 1-2


title: Flp-In 293 T-REx, CLIP-UPF1 R843C, siNT, rep 3


title: RBG26443_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 R843C, siNT, rep 2


title: RBG26442_Plate_4_WT


title: RBG26440_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 R843C, siNT, rep 1


title: Gclc WT 3 Batch 1-1


title: Gclc WT 3 Batch 2-1


title: RBG26441_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 K498A, siUPF1, rep 3


title: RBG26446_Plate_4_WT


title: Gclc WT 2 Batch 1-2


title: Flp-In 293 T-REx, CLIP-UPF1 K498A, siUPF1, rep 2


title: RBG26447_Plate_4_WT


title: Gclc WT 2 Batch 2-1


title: Flp-In 293 T-REx, CLIP-UPF1 K498A, siUPF1, rep 1


title: RBG26445_Plate_4_WT


title: RBG26444_Plate_4_WT


title: Gclc KO 2 Batch 2-2


title: Gclc WT 2 Batch 1-1


title: Flp-In 293 T-REx, CLIP-UPF1 K498A, siNT, rep 3


title: Flp-In 293 T-REx, CLIP-UPF1 K498A, siNT, rep 2


title: Gclc KO 2 Batch 1-2


title: Flp-In 293 T-REx, CLIP-UPF1 K498A, siNT, rep 1


title: Gclc KO 2 Batch 2-1


title: Gclc WT 2 Batch 2-2


title: Flp-In 293 T-REx, CLIP-UPF1 GA-KH, siUPF1, rep 3


title: RBG26432_Plate_4_WT


title: Gclc KO 2 Batch 1-1


title: RBG26435_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 GA-KH, siUPF1, rep 2


title: RBG26433_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 GA-KH, siUPF1, rep 1


title: Gclc KO 1 Batch 1-2


title: RBG26438_Plate_4_KO


title: Gclc KO 1 Batch 2-2


title: RBG26439_Plate_4_KO


title: Gclc KO 1 Batch 2-1


title: Flp-In 293 T-REx, CLIP-UPF1 GA-KH, siNT, rep 1


title: Gclc KO 1 Batch 1-1


title: Gclc WT 1 Batch 2-2


title: RBG26437_Plate_4_KO


title: RBG26434_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siUPF1, rep 3


title: Gclc WT 1 Batch 1-2


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siUPF1, rep 2


title: RBG26427_Plate_4_KO


title: RBG26426_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siNT, rep 3


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siUPF1, rep 1


title: Gclc WT 1 Batch 1-1


title: RBG26425_Plate_4_KO


title: RBG26424_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 GA-KH, siNT, rep 3


title: Gclc WT 1 Batch 2-1


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siNT, rep 1


title: Flp-In 293 T-REx, CLIP-UPF1 GA-KH, siNT, rep 2


title: Flp-In 293 T-REx, CLIP-UPF1 E797R, siNT, rep 2


title: WT_3

city: Erlangen

first: Pang

last: Lyu

address: Glückstr. 6

department: Department of Internal Medicine 3

institute: University Hospital Erlangen

data_processing:
Nanodrop: Preliminary quantitation
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Agarose Gel Electrophoresis: tests RNA degradation and potential contamination
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Paired-end sequencing libraries are sequenced by Illumina high-throughput sequencer.
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
small intestine were dissected and small intestine epithelial cells was isolated from collagen induced arthritis model, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total
RNA libraries were prepared for sequencing using standard Illumina protocols

value: small intestine epithelial cells

tag: strain

value: HIF[alpha]F/F(Littermate control)

value: naïve mice


title: RBG26436_Plate_4_KO

value: bone marrow

value: ESLAM


title: RBG26431_Plate_4_WT

value: WT


title: Flp-In 293 T-REx, CLIP-UPF1 DE636AA, siUPF1, rep 3


title: WT_2


title: WT_1


title: RBG26430_Plate_4_WT


title: KO2a_3


title: RBG26429_Plate_4_KO


title: RBG26428_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 DE636AA, siUPF1, rep 2


title: KO2a_2


title: Flp-In 293 T-REx, CLIP-UPF1 DE636AA, siUPF1, rep 1


title: KO2a_1


title: Flp-In 293 T-REx, CLIP-UPF1 DE636AA, siNT, rep 3


title: RBG26418_Plate_4_WT


title: KO1a_3


title: Flp-In 293 T-REx, CLIP-UPF1 DE636AA, siNT, rep 2


title: RBG26417_Plate_4_KO


title: Flp-In 293 T-REx, CLIP-UPF1 DE636AA, siNT, rep 1


title: KO1a_1


title: KO1a_2


title: Flp-In 293 T-REx, CLIP, siUPF1, rep 3


title: RBG26416_Plate_4_KO


title: RBG26423_Plate_4_WT


title: RBG26421_Plate_4_WT


title: RBG26422_Plate_4_WT


title: RING1BmAID-TAF1dTAG-T7-Input-AUX-rep3

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: Input for TAF1-T7 ChIP-seq in cells  treated with IAA to depleted RING1B-mAID.

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+hg19) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
Sequencing datasets were calibrated to the spike-in human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools.
Assembly: mm10; hg19
Supplementary files format and content: Genome coverage tracks were generated using the pileup function from MACS2.
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

organism:
Homo sapiens
Mus musculus

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
5 x 10^7 ESCs were fixed with 1% formaldehyde (methanol-free, Thermo Fisher Scientific) for 10 min at 25⁰C. Fixation was quenched using glycine added to 125 mM. Cells were then pelleted at 1000xg for 5 min and washed with PBS. Cross-linked ESCs were mixed with 1 x 10^6 cross-linked HEK 293T/T7-SCC1 cells (1% formaldehyde for 10 min; a gift from Martin Houlard, Nasmyth lab). Chromatin was prepared by incubation in 1 ml FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x PIC, 10 mM NaF) on ice for 10 min. Chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode) at 4⁰C for 23 cycles (30s on/off) to an average size of 0.5 kb. The sonicated material was pelleted at 20,000xg for 20 min, and the supernatant taken as sonicated chromatin. 300 μg chromatin was used per IP. Chromatin was diluted to 1 ml total volume per IP in FA-lysis buffer. An additional volume of diluted chromatin was taken to use as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in 1x TE buffer at 4⁰C for 1 hr. Chromatin was pre-cleared with agarose beads (40 μl slurry beads per ChIP) at 4⁰C for 1 - 2 hr. The input sample was taken from the pre-cleared chromatin, and the remainder was immunoprecipitated overnight at 4⁰C with 5μl T7 (Cell Signalling, D9E1X). Antibody-bound chromatin was precipitated for 3 hr at 4⁰C using 40 μl slurry of blocked Protein A agarose beads. Washes were carried out for 5 min each at 4⁰C, using ice-cold FA-lysis buffer, FA-lysis buffer with 500 mM NaCl, 1x DOC buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 1 mM EDTA , 0.5% NP-40, 0.5% Na-deoxycholate), and 2 washes with TE buffer. DNA was eluted in elution buffer (1% SDS and 0.1 M NaHCO3). Cross-links were reversed for ChIPs and inputs at 65⁰C overnight with 200 mM NaCl and 2 μl RNase A (Sigma). Samples were then incubated with 20 μg Proteinase K for 1 hr at 45⁰C. DNA for ChIPs and inputs was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). Purified DNA was analysed using ChIP-qPCR.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate on Illumina NextSeq 500 platform.

treatment_protocol: Cell lines expressing were treated with 100 nM dTAG-13 (Tocris Bioscience) or 500 µM IAA (Sigma) for 4 hours to induce protein depletion.

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in.

value: 500 µM IAA

tag: treatment time

tag: replicate

tag: spike-in reference

value: Homo sapiens

tag: spike-in cell_line

value: HEK293T; Scc1-T7


title: Flp-In 293 T-REx, CLIP, siUPF1, rep 2

value: Flp-In 293 T-REx cell line

tag: treatment


title: Flp-In 293 T-REx, CLIP, siUPF1, rep 1


title: RBG26420_Plate_4_WT


title: Flp-In 293 T-REx, CLIP, siNT, rep 2

value: non-targeting siRNA


title: Flp-In 293 T-REx, CLIP, siNT, rep 3


title: RBG26419_Plate_4_WT


title: RING1BmAID-TAF1dTAG-T7-Input-UNT-rep3

description: Input for untreated control for TAF1-T7 ChIP-seq in RING1BminiAID;TAF1-T7-dTAG mESCs

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in. Untreated control for TAF1-T7 ChIP-seq in RING1BminiAID;TAF1-T7-dTAG mESCs

value: untreated


title: RING1BmAID-TAF1dTAG-T7-Input-AUX-rep1


title: RBG26412_Plate_4_KO

value: KO


title: Flp-In 293 T-REx, CLIP, siNT, rep 1


title: RBG26413_Plate_4_KO


title: RING1BmAID-TAF1dTAG-T7-Input-UNT-rep2


title: Flp-In 293 T-REx, CLIP-UPF1 A546H, siUPF1, rep 2

value: UPF1 siRNA


title: Flp-In 293 T-REx, CLIP-UPF1 A546H, siUPF1, rep 3


title: RING1BmAID-TAF1dTAG-T7-AUX-rep2

description:
Cells treated with IAA to depleted RING1B-mAID.
RING1BmAID_TAF1dTAG_T7_AUX.mm10.normalisedSpikeInInput.MERGED.MACS2.bw

value: anti-T7 (Cell Signalling D9E1X)


title: RING1BmAID-TAF1dTAG-T7-Input-AUX-rep2


title: RBG26415_Plate_4_KO


title: RING1BmAID-TAF1dTAG-T7-AUX-rep3


title: RBG26408_Plate_4_WT


title: RING1BmAID-TAF1dTAG-T7-AUX-rep1


title: RBG26409_Plate_4_WT


title: Flp-In 293 T-REx, CLIP-UPF1 A546H, siNT, rep 2


title: Flp-In 293 T-REx, CLIP-UPF1 A546H, siNT, rep 3


title: RING1BmAID-TAF1dTAG-T7-UNT-rep3

description:
Untreated control for TAF1-T7 ChIP-seq in RING1BminiAID;TAF1-T7-dTAG mESCs
RING1BmAID_TAF1dTAG_T7_UNT_mm10.normalisedSpikeInInput.MERGED.MACS2.bw


title: Flp-In 293 T-REx, CLIP-UPF1 A546H, siUPF1, rep 1


title: Flp-In 293 T-REx, CLIP-UPF1 A546H, siNT, rep 1


title: RING1BmAID-TAF1dTAG-T7-UNT-rep2